public void testBasicStructure() throws Exception {
parser.processOntology(
new InputStreamReader(
getClass().getClassLoader().getResourceAsStream("OboParserTest.obo")));
Set terms = parser.getOboTerms();
// assertEquals("GO:0000004", ((OboTerm) terms.iterator().next()).getId());
terms = new HashSet(parser.terms.values());
assertEquals(4, terms.size()); // 4 terms total
OboTerm dt1 = (OboTerm) parser.terms.get("GO:0000001");
OboTerm dt2 = (OboTerm) parser.terms.get("GO:0000002");
OboTerm dt3 = (OboTerm) parser.terms.get("GO:0000003");
OboTerm dt4 = (OboTerm) parser.terms.get("GO:0000004");
assertNotNull(dt1);
assertNotNull(dt2);
assertNotNull(dt3);
assertNotNull(dt4);
// assertTrue(dt1.getChildren().contains(dt2));
// assertTrue(dt1.getChildren().contains(dt4));
// assertTrue(dt2.getChildren().contains(dt3));
// assertTrue(dt1.getComponents().contains(dt3));
}
public void testNamespaces() throws Exception {
parser.processOntology(
new InputStreamReader(
getClass().getClassLoader().getResourceAsStream("OboParserTest.obo")));
OboTerm dt1 = (OboTerm) parser.terms.get("GO:0000001");
OboTerm dt2 = (OboTerm) parser.terms.get("GO:0000002");
OboTerm dt3 = (OboTerm) parser.terms.get("GO:0000003");
assertEquals("gene_ontology", dt1.getNamespace());
assertEquals("other_namespace", dt2.getNamespace());
assertEquals("gene_ontology", dt3.getNamespace());
}
public void testDescriptions() throws Exception {
parser.processOntology(
new InputStreamReader(
getClass().getClassLoader().getResourceAsStream("OboParserTest.obo")));
OboTerm dt1 = (OboTerm) parser.terms.get("GO:0000001");
OboTerm dt2 = (OboTerm) parser.terms.get("GO:0000002");
OboTerm dt3 = (OboTerm) parser.terms.get("GO:0000003");
assertEquals("iosis, mediated byhe cytoskeleton.", dt1.getDescription());
assertEquals(
"The maintenance of the structure and integrity of the mitochondrial genome.",
dt2.getDescription());
assertEquals("", dt3.getDescription());
}
public void testGetTermIdNameMap() throws Exception {
String test =
IOUtils.toString(getClass().getClassLoader().getResourceAsStream("OboParserTest.obo"));
Map idNames = parser.getTermIdNameMap(new StringReader(test));
HashMap expecting = new HashMap();
expecting.put("GO:0000001", "mitochondrion inheritance");
expecting.put("GO:0000002", "mitochondrial genome maintenance");
expecting.put("GO:0000003", "reproduction");
expecting.put("GO:0000004", "partoftest");
assertEquals(expecting, idNames);
}
public void testSynonyms() throws Exception {
parser.processOntology(
new InputStreamReader(
getClass().getClassLoader().getResourceAsStream("OboParserTest.obo")));
OboTerm dt3 = (OboTerm) parser.terms.get("GO:0000003");
assertEquals(6, dt3.getSynonyms().size());
HashSet expSyns = new LinkedHashSet();
expSyns.add(new OboTermSynonym("some_value", "synonym"));
expSyns.add(new OboTermSynonym("related_value", "related_synonym"));
expSyns.add(new OboTermSynonym("exact_value", "exact_synonym"));
expSyns.add(new OboTermSynonym("broad_value", "broad_synonym"));
expSyns.add(new OboTermSynonym("narrow_value", "narrow_synonym"));
expSyns.add(new OboTermSynonym("GO:0019952", "alt_id"));
assertEquals(expSyns, dt3.getSynonyms());
}
public void testAddSynonyms() throws Exception {
OboTerm term = new OboTerm("id", "name");
parser.addSynonyms(
term,
Arrays.asList(
new String[] {
"\"no escapes\" []",
" \"one \\\" escape\" [asdf]",
" \"late quotes\" [as\\\"df] \"",
"\"nothing trailing\""
}),
"synonym_type");
assertEquals(4, term.getSynonyms().size());
HashSet expect = new HashSet();
expect.add(new OboTermSynonym("no escapes", "synonym_type"));
expect.add(new OboTermSynonym("one \" escape", "synonym_type"));
expect.add(new OboTermSynonym("late quotes", "synonym_type"));
expect.add(new OboTermSynonym("nothing trailing", "synonym_type"));
assertEquals(expect, term.getSynonyms());
}
public void testXrefs() throws Exception {
OboTerm term = new OboTerm("id", "name");
parser.readConfig();
parser.addXrefs(term, Arrays.asList(new String[] {"FBbt:000", "monkey"}));
assertEquals(1, term.getXrefs().size());
}
public void testDodgySynonym() {
OboTerm term = new OboTerm("id", "name");
parser.addSynonyms(term, Arrays.asList(new String[] {"xxxxxxxx"}), "synonym_type");
assertEquals(0, term.getSynonyms().size());
}
public void testUnescape() {
assertEquals("\n", parser.unescape("\\n"));
assertEquals(" ", parser.unescape("\\W"));
assertEquals("\t", parser.unescape("\\t"));
assertEquals(":", parser.unescape("\\:"));
assertEquals(",", parser.unescape("\\,"));
assertEquals("\"", parser.unescape("\\\""));
assertEquals("\\", parser.unescape("\\\\"));
assertEquals("()", parser.unescape("\\(\\)"));
assertEquals("[]", parser.unescape("\\[\\]"));
assertEquals("{}", parser.unescape("\\{\\}"));
// pass-thru
assertEquals("\n", parser.unescape("\n"));
assertEquals(" ", parser.unescape(" "));
assertEquals("\t", parser.unescape("\t"));
assertEquals(":", parser.unescape(":"));
assertEquals(",", parser.unescape(","));
assertEquals("\"", parser.unescape("\""));
assertEquals("()", parser.unescape("()"));
assertEquals("[]", parser.unescape("[]"));
assertEquals("{}", parser.unescape("{}"));
assertEquals(
"a\\bc:d,e[f)g{h i\tj\nk", parser.unescape("a\\\\b\\c\\:d\\,e\\[f\\)g\\{h\\Wi\\tj\\nk"));
}
